Issues with find.enrichment.py when I use the same IDs for study.txt and population.txt

[pomorale]

I am running find_enrichment.py of a Denovo transcriptome assembly, and I want to have it as a description of the GO abundance in my nonmodel plant transcriptome. Given that my IDs are unknown, I created a population list with all my Trinity IDs and a study list with the same terms. My association list comes from a functional analysis with Interproscan. I did this because I want to maintain the original IDs.

My Issues with find.enrichment.py when I use the duplicate IDs for study.txt and population.txt. My output is that says that GO terms were found but need to be written. I used the --pval=-1 to write regardless the value, and I did not give me any list to work with.

Thanks

[tanghaibao]

@pomorale

I created a population list with all my Trinity IDs and a study list with the same terms

This is a strange set up.

You have provided the same gene list on both sides so I'd expect that no GO terms will show any difference in the study.

Is there a subset of the total genes that you are interested in, i.e. the "study" set?